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Abstract Background Supportive periodontal therapy (SPT) must take individual patient risk factors into account. We conducted a multicenter joint retrospective cohort study to investigate the value of modified periodontal risk assessment (MPRA) and therapy-resistant periodontitis (TRP) assessment as predictive factors for tooth loss due to periodontal disease in patients with severe periodontitis during SPT. Methods The subjects were 82 patients from 11 dental institutions who were diagnosed with severe periodontitis and continued SPT for at least 1 year (mean follow-up = 4.9 years) between 1981 and 2008. The outcome was tooth loss due to periodontal disease during SPT. The Cox proportional hazards model was used to analyze sex, age, diabetes status, smoking history, number of periodontal pockets measuring ≥6 mm, rate of bleeding on probing, bone loss/age ratio, number of teeth lost, MPRA, and TRP assessment as explanatory variables. Results Univariate analysis showed that loss of ≥8 teeth by the start of SPT [hazard ratio (HR) 2.86], MPRA score indicating moderate risk (HR 8.73) or high risk (HR 11.04), and TRP assessment as poor responsiveness to treatment (HR 2.79) were significantly associated with tooth loss (p